Controlled translocation of macromolecules employing a funnel nanopore structure and a gel

ABSTRACT

A system of controlled translocation of macromolecules by gel electrophesis employs a funnel nanopore structure. A graphene portion is attached to a porous material layer including funnel-shaped pores such that the graphene portion blocks the side of the porous material layer having openings for smaller pores. A pair of electrical contacts is formed on the graphene portion. A dielectric material layer may be deposited to hold the graphene portion in place. A nanoscale hole is formed through the dielectric material layer and the graphene portion to provide a smallest opening in a funnel nanopore structure. The funnel nanopore structure is placed within a capsule configured for gel electrophoresis. A linear chain of molecules can pass through a funnel-shaped pore and the nanoscale hole during the gel electrophoresis. A graphene nanopore detector allows measurement of blockage current for sufficient resolution of base pairs in DNA&#39;s.

BACKGROUND

The present disclosure generally relates to a method of translocatingmacromolecules, and particularly to a method of translocatingmacromolecules employing a funnel nanopore structure and a gel, andstructures and apparatuses for affecting the same.

Many macromolecules including deoxyribonucleic acid (DNA) have a shapeof a linear chain and are conducive to sequencing. In order to providesequencing of a linear chain of a macromolecule, however, themacromolecule must be allowed to move along the direction of thelengthwise chain. Thus, a method of geometrically orientating a linearchain of a macromolecule with respect to a measurement device isdesired.

SUMMARY

A system of controlled translocation of macromolecules by gelelectrophoresis employs a funnel nanopore structure. A graphene portionis attached to a porous material layer including funnel-shaped poressuch that the graphene portion blocks the side of the porous materiallayer having openings for smaller pores relative to pores on theopposite side. A pair of electrical contacts is formed on the grapheneportion. A dielectric material layer may be deposited to hold thegraphene portion in place. A nanoscale hole is formed through thedielectric material layer and the graphene portion to provide a smallestopening in a funnel nanopore structure. The funnel nanopore structure isplaced within a capsule configured for gel electrophoresis. A linearchain of molecules can pass through a funnel-shaped pore and thenanoscale hole during the gel electrophoresis, and a change in ablockage current in a circuit including the graphene portion can bemeasured as the linear chain passes through the opening to collectinformation on the structure of the macromolecule. A graphene nanoporedetector allows measurement of blockage current for sufficientresolution of base pairs in DNA's.

According to an aspect of the present disclosure, a gel electrophoresisapparatus is provided. The gel electrophoresis apparatus includes anenclosure divided into a first chamber and a second chamber by a dividerplate. The divider plate includes a porous material layer includingfunnel-shaped pores between a first side surface and a second sidesurface, wherein each of the funnel-shaped pores has a smaller openingat the first side surface than at the second side surface, and agraphene portion contacting the first side surface, wherein a nanoscalehole extends through the graphene portion and to one of thefunnel-shaped pores. A first electrode is provided in the first chamber,and a second electrode is provided in the second chamber. Further, acircuitry configured to provide a voltage across the first electrode andthe second electrode is also provided.

According to another aspect of the present disclosure, a structure isprovided, which includes a porous material layer including funnel-shapedpores between a first side surface and a second side surface, whereineach of the funnel-shaped pores has a smaller opening at the first sidesurface than at the second side surface. The structure further includesa graphene portion contacting the first side surface, wherein ananoscale hole extends through the graphene portion and to one of thefunnel-shaped pores.

According to yet another aspect of the present disclosure, a method ofoperating an apparatus is provided. An apparatus is provided, whichincludes an enclosure divided into a first chamber and a second chamberby a divider plate, the divider plate including a porous material layerincluding funnel-shaped pores between a first side surface and a secondside surface. The first side surface is a peripheral surface of thefirst chamber and the second side surface is a peripheral surface of thesecond chamber, and each of the funnel-shaped pores has a smalleropening at the first side surface than at the second side surface. Theenclosure is filled with a sol. The sol is converted into a gel.Macromolecules including a linear chain are inserted into the firstchamber. The macromolecules are induced to pass through the dividerplate by performing gel electrophoresis across the first chamber and thesecond chamber.

BRIEF DESCRIPTION OF SEVERAL VIEWS OF THE DRAWINGS

FIG. 1A is a vertical cross-sectional view of a first exemplarystructure including a porous material layer including funnel-shapedpores according to an embodiment of the present disclosure.

FIG. 1B is a bottom side view of the first exemplary structure of FIG.1A. The A-A′ plane refers to the plane of the vertical cross-section ofFIG. 1A.

FIG. 1C is a top side view of the first exemplary structure of FIG. 1A.The A-A′ plane refers to the plane of the vertical cross-section of FIG.1A.

FIG. 2A is a vertical cross-sectional view of the first exemplarystructure after disposing a graphene portion on a bottom surface of theporous material layer according to an embodiment of the presentdisclosure.

FIG. 2B is a bottom side view of the first exemplary structure of FIG.2A. The A-A′ plane refers to the plane of the vertical cross-section ofFIG. 2A.

FIG. 3A is a vertical cross-sectional view of the first exemplarystructure after formation of contact structures on the graphene portionaccording to an embodiment of the present disclosure.

FIG. 3B is a bottom side view of the first exemplary structure of FIG.3A. The A-A′ plane refers to the plane of the vertical cross-section ofFIG. 3A.

FIG. 4A is a vertical cross-sectional view of the first exemplarystructure after formation of a dielectric material layer according to anembodiment of the present disclosure.

FIG. 4B is a bottom side view of the first exemplary structure of FIG.4A. The A-A′ plane refers to the plane of the vertical cross-section ofFIG. 4A.

FIG. 5A is a vertical cross-sectional view of the first exemplarystructure after formation of a nanoscale hole through the dielectricmaterial layer and the graphene portion according to an embodiment ofthe present disclosure.

FIG. 5B is a bottom side view of the first exemplary structure of FIG.5A. The A-A′ plane refers to the plane of the vertical cross-section ofFIG. 5A.

FIG. 6 is a vertical cross-sectional view of a second exemplarystructure after attaching another porous material layer to the grapheneportion or to the dielectric material layer and formation of contactstructures on the graphene portion according to an embodiment of thepresent disclosure.

FIG. 7 is a schematic view illustrating an exemplary gel electrophoresisapparatus employing the first exemplary structure or the secondexemplary structure as a divider plate according to an embodiment of thepresent disclosure.

DETAILED DESCRIPTION

As stated above, the present disclosure relates to a method oftranslocating macromolecules, and particularly to a method oftranslocating macromolecules employing a funnel nanopore structure and agel, and structures and apparatuses for effecting the same. Aspects ofthe present disclosure are now described in detail with accompanyingfigures. It is noted that like reference numerals refer to like elementsacross different embodiments. The drawings are not necessarily drawn toscale. As used herein, ordinals such as “first,” “second,” and “third,”etc. are employed to distinguish similar elements, and a same elementmay be labeled with different ordinals across the specification and theclaims.

Referring to FIGS. 1A, 1B, and 1C, a first exemplary structure accordingto an embodiment of the present disclosure includes a porous materiallayer 10 including funnel-shaped pores 11. As used herein, a“funnel-shaped pore” refers to a pore extending to at least one openingin a surface of a matrix structure in which the pore is embedded suchthat a cross-sectional area of an end portion of the pore decreasestoward each of the at least one opening. Each funnel-shaped pore 11 inthe porous material layer 10 includes at least one tapered portion inwhich the cross-sectional area decreases with distance from ageometrical center of the funnel-shaped pore 11. As used herein, ageometrical center of a pore refers to a point corresponding to themathematical average of all Cartesian coordinates of the pore. Eachfunnel-shaped pore 11 extends from the front side (the top side in FIG.1A and shown in FIG. 1C) of the porous material layer 10 to the backside (the bottom side in FIG. 1A and shown in FIG. 1B) of the porousmaterial layer 10. The back surface is herein referred to as a firstside surface (i.e., a surface that is on a first side), and the frontsurface is herein referred to as a second side surface (i.e., a surfacethat is on a second side). Each funnel-shaped pore 11 can extend betweenthe first side surface and the second side surface. Each funnel-shapedpore 11 includes one opening on the front side, and at least one openingon the back side. A funnel-shaped pore 11 can include a plurality ofopenings on the back side, i.e., can be multi-pronged pores such thatmultiple tapered portions are adjoined to a main cavity having a greaterlateral dimension. Each of the funnel-shaped pores 11 can have a smalleropening at the first side surface than at the second side surface.

The porous material layer 10 includes a dielectric material. In oneembodiment, the porous material layer 10 can consist essentially of adielectric material. In one embodiment, the porous material layer 10 canconsist essentially of a dielectric ceramic material. In one embodiment,the porous material layer 10 can consist essentially of a dielectricmetal oxide. In one embodiment, the porous material layer 10 can includealuminum oxide (Al₂O₃).

In one embodiment, the porous material layer 10 can consist essentiallyof aluminum oxide. In one embodiment, each funnel-shaped pore 11 mayinclude a substantially uniform pore portion in which a cross-sectionalarea does not change substantially (i.e., by more than 20%), and atleast one tapered portion in which the cross-sectional area decreaseswith distance from a geometrical center of the funnel-shaped pore 11. Inone embodiment, the average of lateral dimensions of the substantiallyuniform pore portion is herein referred to as a first lateral dimensiond1. The first lateral dimension d1 may be the average of diameters ormajor axes of the horizontal cross-sectional areas (i.e., across-sectional area within a plane that is parallel to the first sidesurface and the second side surface) of the substantially uniform poreportions if the horizontal cross-sectional areas have circular orelliptical shapes. In one embodiment, the first lateral dimension d1 maybe in a range from 50 nm to 800 nm at the second side surface (as seenin FIG. 1C) and throughout the substantially uniform pore portion,although lesser and greater dimensions can also be employed. In oneembodiment, the first lateral dimension d1 may greater than 100 nm. Inanother embodiment, the first lateral dimension d1 may be greater than200 nm. In one embodiment, the first lateral dimension d1 may be lessthan 200 nm. In another embodiment, the first lateral dimension d1 maybe less than 100 nm.

The average of the lateral dimensions of openings of the funnel-shapedpore 11 at the first side surface (as seen in FIG. 1B) is hereinreferred to as a second lateral dimension d2. The second lateraldimension d2 may be a diameter or a major axis of an opening of afunnel-shaped pore 11 on the first side surface. In one embodiment, thesecond lateral dimension d2 may be in a range from 4 nm to 50 nm at thefirst side surface, although lesser and greater dimensions can also beemployed. In one embodiment, the second lateral dimension d2 may greaterthan 10 nm. In another embodiment, the second lateral dimension d2 maybe greater than 20 nm. In one embodiment, the second lateral dimensiond2 may be less than 20 nm. In another embodiment, the second lateraldimension d2 may be less than 10 nm.

The thickness of the substantially uniform pore portions, i.e., thedimension of the substantially uniform pore portions as measured along adirection perpendicular to the first side surface and the second sidesurface, is herein referred to as a first thickness t1. The firstthickness t1 may be in a range from 20 microns to 500 microns, althoughlesser and greater thicknesses can also be employed. In one embodiment,the first thickness t1 can be greater than 30 microns. In anotherembodiment, the first thickness t1 can be greater than 40 microns. Inone embodiment, the first thickness t1 can be less than 200 microns. Inanother embodiment, the first thickness t2 can be less than 100 microns.

The thickness of the tapered portions of the funnel-shaped pores 11,i.e., the dimension of the tapered portions as measured along adirection perpendicular to the first side surface and the second sidesurface, is herein referred to as a second thickness t2. The secondthickness t2 may be in a range from 20 nm to 100 nm, although lesser andgreater thicknesses can also be employed.

The lateral dimension of the porous material layer 10, i.e., the extentof the porous material layer 10 within the plane of the first sidesurface or within the plane of the second side surface, can be in arange from 0.5 cm to 10 cm, although lesser and greater dimensions canalso be employed.

In one embodiment, a commercially available product may be employed asthe porous material layer 10. For example, Whatman® Anotop® 10 syringefilters made of aluminum oxide and commercially available from WhatmanGmbH may be employed as the porous material layer 10 for the purpose ofthe present disclosure. The total thickness (i.e., t1+t2) of the porousmaterial layer 10 as provided may be about 53 microns, and the firstlateral dimension d1 may be about 200 nm, and the second lateraldimension d2 may be about 25 nm.

In one embodiment, the porous material layer 10 may be coated with adielectric material layer (not shown) to reduce the size of the secondlateral dimension. The dielectric material layer includes a dielectricmaterial that may be conformally deposited by atomic layer deposition(ALD) or chemical vapor deposition (CVD). The dielectric material can bea dielectric metal oxide such as aluminum oxide, titanium oxide, hafniumoxide, zirconium oxide, or can be a dielectric semiconductor oxide suchas silicon oxide, or can be a dielectric metal nitride, or can be adielectric semiconductor nitride such as silicon nitride. The thicknessof the deposited dielectric material layer is selected such that theopenings at the first side surface of the funnel-shaped pores are notsealed by the dielectric material layer. The second lateral dimension d2after deposition of the dielectric material layer can be in a range from4 nm to 20 nm, although lesser and greater second lateral dimensions d2can also be employed.

Referring to FIGS. 2A and 2B, at least one graphene portion 20 isdisposed on the first side surface of the porous material layer 10. Eachgraphene portion 20 is a piece of a graphene sheet that is patternedinto a suitable shape, for example, by cutting. A graphene sheet can beprovided by any method known in the art, and is patterned, for example,by cutting with a sharp instrument such as a pair of scissors or anothercutting device, into one or more of the graphene portions 20. Eachgraphene portion 20 can have a polygonal shape (such as a rectangularshape), or a curvilinear shape in which at least one edge has a curvedprofile. The lateral dimensions of a graphene portion 20 can be in arange from 100 microns to 3 mm, although lesser and greater dimensionscan also be employed. In an illustrative example, each graphene portion20 can have a rectangular shape such that the length of the rectanglecan be 1 mm and the width of the rectangle can be 100 microns. The atleast one graphene portion 20 may be disposed on the first side surfaceof the porous material layer 10 in air, in vacuum, or in a solution fromwhich a combination of the at least one graphene portion 20 and theporous material layer 10 can be scooped. In one embodiment, a singlegraphene portion 20 may be disposed on the porous material layer 10. Inanother embodiment, a plurality of graphene portions 20 may be disposedon the porous material layer 10.

Referring to FIGS. 3A and 3B, a pair of contact structures (22A, 22B) isformed on each graphene portion 20. The pair of contact structures (22A,22B) includes a first contact structure 22A and a second contactstructure 22B that are laterally spaced from each other. In oneembodiment, the first contact structure 22A and the second contactstructure 22B can be formed on opposite sides of the graphene portion 20with respect to a geometrical center of the graphene portion 20. Thus,the pair of contact structures (22A, 22B) is in physical contact withtwo regions of the graphene portion 20.

The pair of contact structures (22A, 22B) includes a material that formsa metallurgical contact with the graphene portion 20. Non-limitingexamples of metallic materials that can be employed for the pair ofcontact structures (22A, 22B) include gold, palladium, tungsten,titanium, alloys thereof, and combinations thereof. The lateraldimensions of each contact structure (22A, 22B) can be in a range from 1micron to 10 microns, although lesser and greater dimensions can also beemployed. The pair of contact structures (22A, 22B) may be formed, forexample, by a masked evaporation process, a masked sputtering process,or any other known method for forming metallurgical contacts on agraphene sheet. A pair of conductive lead wires (24A, 24B) is attachedto the pair of contact structures (22A, 22B). A first conductive leadwire 24A can be attached to the first contact structure 22A, and asecond conductive lead wire 24B can be attached to the second contactstructure 22B. The first conductive lead wire 24A and the secondconductive lead wire 24B can be metal wires, and can be attached to thepair of contact structures (22A, 22B), for example, by soldering or anyother method of attaching a metal wire to a metallic material. The pairof contact structures (22A, 22B) and the pair of conductive lead wires(24A, 24B) can be subsequently employed to measure the blockage currentof the graphene portion 20 as disturbed by a combination of a nanoscalehole (not shown) to be subsequently formed and atoms of a linear chainof a macromolecule (not shown) to pass through the hole during ameasurement step.

Referring to FIGS. 4A and 4B, a dielectric material layer 30 isdeposited on the bottom side of the first exemplary structure.Specifically, the dielectric material layer 30 can be deposited on thephysically exposed surfaces of the at least one graphene portion 20, thecontact structures (22A, 22B), and the physically exposed portions ofthe first side surface of the porous material layer 10. In oneembodiment, an insulation coating may be formed on physically exposedsurfaces of the conductive lead wires (24A, 24B). If a conformaldeposition method such as atomic layer deposition (ALD) or chemicalvapor deposition (CVD) is employed, the dielectric material layer 30 canbe formed on the inner surfaces of the funnel-shaped pores 11. Thus, acoating of the dielectric material layer 30 is formed on the outersurface of each graphene portion 20 and portions of the first sidesurface that are not in contact with the graphene portion 20.

All physically exposed surfaces of each graphene portion 20 can becoated with the dielectric material layer 30. Thus, all surfaces of eachgraphene portion 20 not in contact with the porous material layer 10 arecoated with the dielectric material layer 20. The dielectric materiallayer 30 can include a dielectric metal oxide material such as aluminumoxide, titanium oxide, hafnium oxide, zirconium oxide, lanthanum oxide,or combinations or stacks thereof, and/or can include silicon nitride.The thickness of the dielectric material layer 30 can be in a range from1 nm to 4 nm, although lesser and greater thicknesses can also beemployed. The dielectric material layer 30, in combination with theporous material layer 10, seals each graphene portion 20, and protectseach graphene portion 20 from contaminants during subsequent use of thefirst exemplary structure as a divider plate for a gel electrophoresisapparatus or for other applications. As used herein, “gelelectropheresis” refers to electrophoresis in a gel medium. Further, acoating of the dielectric material layer 30 on the contact structures(22A, 22B) and the conductive lead wires (24A, 24B) provides electricalinsulation for the contact structures (22A, 22B) and the conductive leadwires (24A, 24B). The dielectric material layer 30 can be formed, forexample, by atomic layer deposition (ALD) or chemical vapor deposition(CVD).

Referring to FIGS. 5A and 5B, for each graphene portion 20, a nanoscalehole is formed through the dielectric material layer 30 and the grapheneportion 20. A single nanoscale hole can be formed per each grapheneportion 20. As used herein, a nanoscale hole refers to a hole having alateral dimension in a range from 1 nm to 10 nm. This lateral dimensionis herein referred to as third lateral dimension d3. In one embodiment,the nanoscale hole can have a substantially circular opening area. Inone embodiment, the nanoscale hole may have a diameter in a range from 1nm to 10 nm. In one embodiment, the diameter of the nanoscale hole canbe greater than 1.3 nm. In another embodiment, the diameter of thenanoscale hole can be greater than 1.7 nm. In one embodiment, thediameter of the nanoscale hole can be less than 5 nm. In anotherembodiment, the diameter of the nanoscale hole can be less than 3 nm.

The nanoscale hole may be formed, for example, by an electron beam thatablates the materials of the dielectric material layer 30 and thegraphene portion 20. For example, the electron beam can have an energyin a range from 200 keV to 400 keV, although lesser and greater beamenergies can also be employed. The nanoscale hole extends through thedielectric material layer 30 and through the graphene portion 20. Thenanoscale hole can be formed between the pair of contact structures(22A, 22B). Thus, the distance between the pair of contact structures(22A, 22B) is greater than the distance between the nanoscale hole andany of the pair of contact structures (22A, 22B). In one embodiment, thelocation of the nanoscale hole can be selected such that the nanoscalehole is formed approximately at a geometrical center of the pair ofcontact structures (22A, 22B) so as to maximize disturbance in theballistic transport of electrons between the pair of contact structures(22A, 22B) in the punctured graphene portion 20. The assembly of theporous material layer 10, the at least one graphene portion 20 includinga nanoscale hole, the contact structures (22A, 22B), the conductive leadwires (24A, 24B), and the dielectric material layer 30 is hereincollectively referred to as a plate structure 100, which is subsequentlyemployed as a divider plate between two chambers in a gelelectrophoresis apparatus.

Referring to FIG. 6, a second exemplary structure can be derived fromthe first exemplary structure by attaching another porous material layer(which is herein referred to as a second porous material layer 10′) tothe at least one graphene portion 20, or to the dielectric materiallayer 30. The second porous material layer 10′ can have any of thegeometrical features that the porous material layer 10 described abovecan have. Further, the second porous material layer 10′ can have anycomposition that the porous material layer 10 described above can have.The composition of the porous material layer 10 and the second porousmaterial layer 10′ may be the same, or different. Particularly, thesecond porous material layer 10′ includes additional funnel-shaped pores11′, which can have the any or all of the geometrical features as thefunnel-shaped pores 11 described above.

The dielectric material layer 30 may, or may not, be employed in thesecond exemplary structure. An assembly of the porous material layer 10,the at least one graphene portion 20 including a nanoscale hole, and theoptional dielectric material layer 30 is formed by performing theprocessing steps of FIGS. 1A-1C, 2A-2B, and 5A-5B without performing theprocessing steps of FIGS. 3A-3B. The processing steps of FIGS. 4A-4Bmay, or may not, be performed. Subsequently, the second porous materiallayer 10′ is disposed directly on the at least one graphene portion 20or indirectly on the at least one graphene portion 20 through thedielectric material layer 30.

The second porous material layer 10′ includes additional funnel-shapedpores 11′ between a surface that contacts the at least one grapheneportion 20 or the dielectric material layer 30 (which is herein referredto as a proximal side surface) and a surface that does not contact theat least one graphene portion 20 or the dielectric material layer 30(which is herein referred to as a distal side surface). The secondporous material layer 10′ is disposed such that tapered portions of theadditional funnel-shaped pores 11′ are closer to the at least onegraphene portion 20 than substantially uniform pore portions of theadditional funnel-shaped pores 11′. The distal side surface is moredistal from the at least one graphene portion 30 than the proximal sidesurface. The proximal surface and the distal surface of the secondporous material layer 10′ can be parallel to the first side surface andthe second side surface of the porous material layer 10. Thus, each ofthe additional funnel-shaped pores 11′ can have a smaller opening at theproximal side surface than at the distal side surface.

The second porous material layer 10′ can be affixed to the first porousmaterial layer 10 by any mechanical means including, but not limited to,at least one clip, an adhesive, at least one screw, at least one boltand at least one nut, external mechanical structures configured to pressagainst the second porous material layer 10′ and the porous materiallayer 10, or a combination thereof.

Each graphene portion 20 can be sized so that end regions of thegraphene portion 20 protrude out of the peripheries of the porousmaterial layer 10 and/or peripheries of the second porous material layer10′. A pair of contact structures (22A, 22B) can subsequently be formedon each graphene portion 20. The pair of contact structures (22A, 22B)includes a first contact structure 22A and a second contact structure22B that are laterally spaced from each other. In one embodiment, thefirst contact structure 22A and the second contact structure 22B can beformed on opposite sides of the graphene portion 20 with respect to ageometrical center of the graphene portion 20. Thus, the pair of contactstructures (22A, 22B) is in physical contact with two regions of thegraphene portion 20. The pair of contact structures (22A, 22B) may beformed on peripheral surfaces of the assembly of the porous materiallayer 10, the second porous material layer 10′, the at least onegraphene portion 20 including a nanoscale hole, the contact structures(22A, 22B), the conductive lead wires (24A, 24B), and the optionaldielectric material layer 30 is herein collectively referred to as aplate structure 100′, which is subsequently employed as a divider platebetween two enclosures in a gel electrophoresis apparatus.

The pair of contact structures (22A, 22B) includes a material that formsa metallurgical contact with the graphene portion 20. Non-limitingexamples of metallic materials that can be employed for the pair ofcontact structures (22A, 22B) include gold, silver, titanium, palladium,tungsten, alloys thereof, and combinations thereof. The lateraldimensions of each contact structure (22A, 22B) can be in a range from 1micron to 10 microns, although lesser and greater dimensions can also beemployed. The pair of contact structures (22A, 22B) may be formed, forexample, by a masked evaporation process, a masked sputtering process,or any other known method for forming metallurgical contacts on agraphene sheet. A pair of conductive lead wires (24A, 24B) is attachedto the pair of contact structures (22A, 22B). A first conductive leadwire 24A can be attached to the first contact structure 22A, and asecond conductive lead wire 24B can be attached to the second contactstructure 22B. The first conductive lead wire 24A and the secondconductive lead wire 24B can be metal wires, and can be attached to thepair of contact structures (22A, 22B), for example, by soldering or anyother method of attaching a metal wire to a metallic material. The pairof contact structures (22A, 22B) and the pair of conductive lead wires(24A, 24B) can be subsequently employed to measure the blockage currentof the graphene portion 20 as disturbed by a combination of a nanoscalehole (not shown) to be subsequently formed and atoms of a linear chainof a macromolecule (not shown) to pass through the hole during ameasurement step. As used herein, a “blockage current” refers to avariation in electrical current due to passage of an object through ahole in a conductive medium such as a graphene portion.

FIG. 7 illustrates an exemplary gel electrophoresis apparatus employingthe first exemplary structure or the second exemplary structure as adivider plate. Specifically, the plate structure (100 or 100′) describedabove can be employed as the divider plate between two chambers in anenclosure configured for gel electrophoresis. The enclosure includes anenclosure 200, which provides a contiguous sealed space in conjunctionwith a first enclosure opening cap 212 that seals a first enclosureopening 211 and a second enclosure opening cap 222 that seals a secondenclosure opening 221. The enclosure is configured to hold the platestructure (100 or 100′) such that the plate structure (100 or 100′)functions as a divider plate that divides the enclosure into a firstchamber (e.g., the chamber above the plate structure (100 or 100′)) anda second chamber (100 or 100′). In one embodiment, the plate structure(100 or 100′) can be oriented such that the second side surface of theporous material layer 10 faces the first enclosure opening 211 that canbe sealed by the first enclosure opening cap 212. The enclosure is afluidic enclosure to be filled with a gel after a sol/gel transition,and as such, is liquid-tight when sealed.

The enclosure can be in multiple pieces (such as a container and a line)or in a clam shell configuration so that the two chambers of theenclosure can be subsequently accessed for insertion of a firstelectrode 410 into the first chamber and for insertion of a secondelectrode 420 into the second chamber. Alternatively, the firstelectrode 410 can be loaded into the first chamber and the secondelectrode 420 can be loaded into the second chamber before, during, orafter installation of the plate structure (100 or 100′) onto the wallsof the enclosure 200. The first electrode 410 and/or the secondelectrode 420 can be affixed to the walls of the enclosure 200. Theenclosure may be sealed after installation of the plate structure (100or 100′), the first electrode 410, and the second electrode 420, whilemaintaining the ability to remove the first enclosure opening cap 212and the second enclosure opening cap 222.

Conductive lead wires (24A, 24B), which are electrically insulated fromthe environment by an insulator layer (not shown) or by the dielectricmaterial layer 30 (See FIGS. 4A and 4B), are routed to the outside ofthe enclosure through enclosure walls or through a sealed gap (e.g.,between a container and a lid of the enclosure or between a sealingsurface in a clamshell configuration) to current detectors 600configured to measure the blockage current of each graphene portion 20(See FIGS. 5A and 5B) as perturbed by a nanoscale hole in each grapheneportion 20 and a linear chain of a macromolecule to pass therethrough.Each current detector 600 can be configured to provide a predeterminedvoltage and measure the blockage current through an electrical circuitincluding a graphene portion 20, or can be configured to provide apredetermined level of electrical current and measure the voltagerequired to maintain the predetermined level of electrical current.Alternatively, each current detector 600 can be any electrical circuitthat is configured to measure the blockage current of a combination of agraphene portion 20, a nanoscale hole therein, and atoms of a linearchain of a macromolecule to pass through the nanoscale hole. As usedherein, macromolecules refer to macromolecules as known in biochemistry,which include nucleic acids, proteins, carbohydrates, and non-polymericmolecules with large molecular mass such as lipids and macrocycles.

The first electrode 410 and the second electrode 420, if present in thefirst chamber and the second chamber, respectively, at this step, can beelectrically wired to form a portion of a gel electrophoresis circuit.The first electrode 410 can be connected to a variable voltage supplysource 400 by a first insulated wire 412, and the second electrode 420can be connected to the variable voltage supply source 400 by a secondinsulated wire 422. The first insulated wire 412 and the secondinsulated wire 422 can be routed through enclosure walls or through asealed gap (e.g., between a container and a lid of the enclosure orbetween a sealing surface in a clamshell configuration).

The enclosure is subsequently filled with a sol, which is at atemperature above a sol/gel transition temperature. The filling of theenclosure with the sol can be performed, for example, by removing thefirst enclosure opening cap 212 and the second enclosure opening cap222, and by injecting the sol 300 through the first enclosure opening211 while letting a residual gas out of the enclosure 200 through thesecond enclosure opening 221. A gel 300 is subsequently formed in theenclosure 200 after the sol cools below the sol/gel transitiontemperature. The composition of the sol can be selected so that the gel300 subsequently formed has a desired level of pore density and desiredpore sizes therein. For example, the composition of the sol can beselected so that the gel 300 is conducive to gel electrophoresis ofmacromolecules to be transported and analyzed in the exemplary gelelectrophoresis apparatus of the present disclosure. In other words, thepore size and concentration of the gel 300 may be optimized for gelelectrophoresis of the macromolecules. In one embodiment, thecomposition of the sol can be selected so that the gel 300 is conduciveto gel electrophoresis of single strand deoxyribonucleic acid (SSDNA).

If the first electrode 410 and/or the second electrode 420 are notinstalled in the enclosure before injection of the sol, the enclosure isopened and the first electrode 410 and the second electrode 420 areinstalled in the enclosure at this point. A buffer solvent may beoptionally added around the first electrode 410 and/or around the secondelectrode 420. The buffer solvent may be the same solvent that isemployed to form the sol. The buffer solvent may be inserted around thefirst electrode 410 and/or the around the second electrode 420 byopening the first and/or second enclosure opening caps (212, 222) and byinserting a tip of a pipette near the first electrode 410 and/or thesecond electrode 420. The buffer solvent can flow from the pipette intoregions around the first electrode 410 and/or into regions around thesecond electrode 420. The buffer solvent functions as an ionic saltsolution reservoir that prevents the gel 300 from drying.

Macromolecules 500 including a linear chain can be inserted into thefirst chamber, for example, by a pipette. The macromolecules 500 can bedisposed between the first electrode 410 and the plate structure (100 or100′). In one embodiment, the macromolecules can be SSDNA molecules,which are typically negatively charged.

Gel electrophoresis is performed to move the macromolecules 500 throughthe plate structure (100 or 100′) toward the second electrode 420. Thepolarity of the voltage applied across the first electrode 410 and thesecond electrode 420 is selected to enable the movement of themacromolecules 500 away from the first electrode 410 and toward thesecond electrode 420. If the macromolecules 500 have positive electricalcharges, a positive voltage is applied to the first electrode 410 and anegative voltage is applied to the second electrode 420. In this case,the first electrode 410 functions as an anode and the second electrode420 functions as a cathode of the gel electrophoresis process. If themacromolecules 500 have negative electrical charges (as in the case ofDNA strands), a negative voltage is applied to the first electrode 410and a positive voltage is applied to the second electrode 420. In thiscase, the first electrode 410 functions as a cathode and the secondelectrode 420 functions as an anode of the gel electrophoresis process.

The macromolecules 500 are induced to pass through the divider plate,i.e., the plate structure (100 or 100′), by performing gelelectrophoresis across the first chamber and the second chamber of theenclosure. The macromolecules 500 translocate through the portion of thegel 300 in the first chamber, through the plate structure (100 or 100′),and through the portion of the gel 300 in the second chamber. During thegel electrophoresis process, one of the macromolecules 500 is induced topass through a nanoscale hole in one of the at least one grapheneportion 20.

The magnitude of the electrical voltage applied across the firstelectrode 410 and the second electrode 420 is a function of the physicaldimension between the first electrode 410 and the second electrode 420,of the property of the gel 300, and of the desired speed with which alinear chain in a macromolecule 500 passes through a nanoscale hole inone of the at least one graphene portion 20. In an illustrative example,if the physical distance between the first electrode 410 and the secondelectrode 420 is on the order of 1 cm, and if the target speed withwhich a linear chain of a macromolecule 500 passes through a nanoscalehole is about 0.2 nm/msec, the magnitude of the electrical voltage to beapplied across the first electrode 410 and the second electrode 420 canbe in a range from 2 V DC to 10 V DC, although properties of the gel 300can cause this voltage to be greater than 10 V DC or to be less than 2 VDC.

The linear chain of a macromolecule 500 that passes through afunnel-shaped pore 11, a nanoscale hole through a graphene portion 20and optionally through a dielectric material layer 30, and optionallythrough an additional funnel-shaped pore 11′ is linearized at least atthe nanoscale hole due to the geometry of the funnel-shaped pore 11 (andoptionally due to the geometry of the additional funnel-shaped pore 11′)and due to the smaller diameter of the nanoscale hole. Thus, thephysical shape of the portion of the linear chain of the macromolecule500 that passes through a nanoscale hole can be a substantially straightline, which is conducive to characterization of the sequence ofcomponent molecules of the linear chain. This feature is especiallyuseful if the macromolecule 500 that passes through the nanoscale holehas a tendency to curl and/or fold over to form hairpin structures as inthe case of SSDNA or double strand deoxyribonucleic acid (DSDNA). Thus,if an SSDNA molecule passes through the nanoscale hole, the physicalshape of the portion of the SSDNA that passes through a nanoscale holecan be a substantially straight line, and as such, the portion of theSSDNA is conducive to characterization of the base sequence in theSSDNA.

Control of the speed of the translocation of the linear chain of themacromolecule 500 that passes through a nanoscale hole in the exemplarygel electrophoresis apparatus can be easily achieved by changing themagnitude of the electrical voltage across the first electrode 410 andthe second electrode 420. The magnitude of the electrical voltage acrossthe first electrode 410 and the second electrode 420 can be increased toincrease the speed of translocation of the linear chain of themacromolecule 500, and can be decreased to decrease the speed oftranslocation of the linear chain of the macromolecule 500. In oneembodiment, the speed of translocation of the linear chain of themacromolecule 500 can be in a range from 0.05 nm/msec to 0.5 nm/msec,although lesser and greater speeds can also be employed.

While ballistic transport phenomenon exists in each graphene portion 20,the characteristics of the ballistic transport is affected by thepresence of the nanoscale hole and the atoms of the linear chain of themacromolecule 500 that passes through the nanoscale hole. Thus, thedisturbance in electrical resistance of the graphene portion 20 inducedby the macromolecule 500 that pass through the nanoscale hole can bemeasured employing the current detector 600 attached to the grapheneportion 20. The change in the blockage current of the graphene portion20 depends on the type of atoms that is present in the linear chain ofthe macromolecule 500 that passes the nanoscale hole. Thus, the types ofatoms and/or the types of constituent molecules (such as individualbases on an SSDNA) can be characterized employing the exemplary gelelectrophoresis apparatus of the present disclosure.

In case a plurality of graphene portions 20 are employed, the size ofthe nanoscale holes in the graphene portions 20 can be selecteddifferently so that linear chains of macromolecules 500 with differentlateral dimensions can be simultaneously analyzed, or linear chains ofthe same macromolecules 500 may be analyzed with differentsensitivities. Thus, depending on the value of the third lateraldimension d3, which can be in a range from 1 nm to 10 nm, analysis ofmacromolecules 500 having different sizes of linear chains and/oranalysis of macromolecules with different sensitivities are possible.

EXAMPLE

Translocation of DSDNA and SSDNA was demonstrated in 1% agarose gel in0.1M-1 M KCl buffer in an experimental gel electrophoresis apparatusbuilt according to the design of the exemplary gel electrophoresisapparatus illustrated in FIG. 7. The use of a sol/gel medium solves theserious problems associated with DNA interactions with hydrophilic orhydrophobic surfaces. The use of DC electric potential of 2-9 V allowsone to electrophorese the DNA molecules with control speeds (velocity)across a test plate structure 100 at speeds on the order of 0.2 nm/msec.The “trapping” of these molecules in this gel system should allow theratcheting of molecules through the detection device of the system,which includes a graphene portion 20 with a 2 nm nanoscale hole therein.Since the distance between base pairs is 0.5 nanometers the detectorshould have a thickness less than 0.5 nanometers. Such slow speed oftranslocation enabled quantitative measurement of the blockage currentof a graphene portion 20 due to the passage of the SSDNA or DSDNA, whichwas previously impossible due to high speeds of translocation.

In this gel system, the pore size of the gel could be controlled bychanging the concentration of the gel or using gels of smaller pore sizeor cross linking structures (acrylamide). A density gradient of poresize could also be employed. The use of density gradient gels isbelieved to have helped in the linearization of SSDNA for passagethrough the 200 nanometer and 20 nanometer pores and the detector. Thegel was introduced into an enclosure including a plate structure 100with a reservoir on both sides in the heated sol state. Then, the sol(agarose gel made up with buffer) was cooled and the material goesthrough a sol/gel transition. The translocation of both SSDNA and DSDNAthrough a plate structure 100 having a thickness of 53 microns with d1of 200 nm, d2 of 20 nm, and d3 of 2 nm has been demonstrated.

It is noted that the system can also be configured with a combination ofboth gel and sol. Further, it is noted that the sol portions can bedisposed on both sides of the plate structure 100 and around the firstand second electrodes (410, 420) and act as a buffer reservoir andcontact area for the first and second electrodes (410, 420).

While the disclosure has been described in terms of specificembodiments, it is evident in view of the foregoing description thatnumerous alternatives, modifications and variations will be apparent tothose skilled in the art. Each of the various embodiments of the presentdisclosure can be implemented alone, or in combination with any otherembodiments of the present disclosure unless expressly disclosedotherwise or otherwise impossible as would be known to one of ordinaryskill in the art. Accordingly, the disclosure is intended to encompassall such alternatives, modifications and variations which fall withinthe scope and spirit of the disclosure and the following claims.

1. A gel electrophoresis apparatus comprising: an enclosure divided intoa first chamber and a second chamber by a divider plate, said dividerplate comprising: a porous material layer comprising funnel-shaped poresbetween a first side surface and a second side surface, wherein each ofsaid funnel-shaped pores has a smaller opening at said first sidesurface than at said second side surface, and a graphene portioncontacting said first side surface, wherein a nanoscale hole extendsthrough said graphene portion and to one of said funnel-shaped pores; afirst electrode located in said first chamber; a second electrodelocated in said second chamber; and a circuitry configured to provide avoltage across said first electrode and said second electrode.
 2. Thegel electrophoresis apparatus of claim 1, wherein said divider platefurther comprises a coating of a dielectric material layer located on asurface of said graphene portion and portions of said first side surfacethat are not in contact with said graphene portion.
 3. The gelelectrophoresis apparatus of claim 2, wherein said nanoscale holeextends through said dielectric material layer.
 4. The gelelectrophoresis apparatus of claim 1, wherein said porous material layercomprises aluminum oxide, and said funnel-shaped pores have a lateraldimension in a range from 50 nm to 800 nm at said second side surface,and have a lateral dimension in a range from 4 nm to 50 nm at said firstside surface.
 5. The gel electrophoresis apparatus of claim 1, whereinsaid divider plate further comprises: a pair of contact structures inphysical contact with two regions of said graphene portion; and a pairof conductive lead wires in contact with said pair of contactstructures.
 6. The gel electrophoresis apparatus of claim 1, wherein adistance between said pair of contact structures is greater than adistance between said nanoscale hole and any of said pair of contactstructures.
 7. A structure comprising: a porous material layercomprising funnel-shaped pores between a first side surface and a secondside surface, wherein each of said funnel-shaped pores has a smalleropening at said first side surface than at said second side surface; anda graphene portion contacting said first side surface, wherein ananoscale hole extends through said graphene portion and to one of saidfunnel-shaped pores.
 8. The structure of claim 7, further comprising acoating of a dielectric material layer located on a surface of saidgraphene portion and portions of said first side surface that are not incontact with said graphene portion.
 9. The structure of claim 8, whereinsaid nanoscale hole extends through said dielectric material layer. 10.The structure of claim 7, wherein said porous material layer comprisesaluminum oxide, and said funnel-shaped pores have a lateral dimension ina range from 50 nm to 800 nm at said second side surface, and have alateral dimension in a range from 4 nm to 50 nm.
 11. The structure ofclaim 7, further comprising: a pair of contact structures in physicalcontact with two regions of said graphene portion; and a pair ofconductive lead wires in contact with said pair of contact structures.12. The structure of claim 11, wherein a distance between said pair ofcontact structures is greater than a distance between said nanoscalehole and any of said pair of contact structures.
 13. The structure ofclaim 7, further comprising another porous material layer disposeddirectly, or indirectly, on said graphene portion and comprisingadditional funnel-shaped pores between a proximal side surface and adistal side surface that is more distal from said graphene portion thansaid proximal side surface, wherein each of said additionalfunnel-shaped pores has a smaller opening at said proximal side surfacethan at said distal side surface. 14.-20. (canceled)